HEADER TRANSFERASE/INHIBITOR 08-OCT-20 7KDB TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE ADENOSYLTRANSFERASE 2A (MAT2A) TITLE 2 IN COMPLEX WITH SAM AND ALLOSTERIC INHIBITOR COMPOUND 35 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADOMET SYNTHASE 2,METHIONINE ADENOSYLTRANSFERASE 2,MAT 2, COMPND 5 METHIONINE ADENOSYLTRANSFERASE II,MAT-II; COMPND 6 EC: 2.5.1.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MAT2A, AMS2, MATA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ETHIONINE ADENOSYLTRANSFERASE, SAM, ALLOSTERIC INHIBITOR, KEYWDS 2 TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PADYANA,L.JIN REVDAT 3 18-OCT-23 7KDB 1 REMARK REVDAT 2 05-MAY-21 7KDB 1 JRNL REVDAT 1 21-APR-21 7KDB 0 JRNL AUTH Z.KONTEATIS,J.TRAVINS,S.GROSS,K.MARJON,A.BARNETT,E.MANDLEY, JRNL AUTH 2 B.NICOLAY,R.NAGARAJA,Y.CHEN,Y.SUN,Z.LIU,J.YU,Z.YE,F.JIANG, JRNL AUTH 3 W.WEI,C.FANG,Y.GAO,P.KALEV,M.L.HYER,B.DELABARRE,L.JIN, JRNL AUTH 4 A.K.PADYANA,L.DANG,J.MURTIE,S.A.BILLER,Z.SUI,K.M.MARKS JRNL TITL DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR JRNL TITL 2 FOR THE TREATMENT OF TUMORS WITH HOMOZYGOUS MTAP DELETION. JRNL REF J.MED.CHEM. V. 64 4430 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33829783 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01895 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 105550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 5152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.8800 - 3.8500 0.99 3519 194 0.1422 0.1465 REMARK 3 2 3.8500 - 3.0600 1.00 3449 155 0.1150 0.1419 REMARK 3 3 3.0600 - 2.6700 1.00 3429 158 0.1137 0.1220 REMARK 3 4 2.6700 - 2.4300 1.00 3354 197 0.1132 0.1273 REMARK 3 5 2.4300 - 2.2500 1.00 3393 173 0.1087 0.1340 REMARK 3 6 2.2500 - 2.1200 1.00 3363 173 0.1071 0.1033 REMARK 3 7 2.1200 - 2.0200 1.00 3344 178 0.1076 0.1252 REMARK 3 8 2.0200 - 1.9300 1.00 3340 199 0.1084 0.1113 REMARK 3 9 1.9300 - 1.8500 1.00 3363 176 0.1120 0.1172 REMARK 3 10 1.8500 - 1.7900 1.00 3318 176 0.1107 0.1212 REMARK 3 11 1.7900 - 1.7300 1.00 3326 207 0.1098 0.1293 REMARK 3 12 1.7300 - 1.6800 1.00 3343 169 0.1102 0.1353 REMARK 3 13 1.6800 - 1.6400 1.00 3361 169 0.1127 0.1149 REMARK 3 14 1.6400 - 1.6000 1.00 3332 177 0.1143 0.1374 REMARK 3 15 1.6000 - 1.5600 1.00 3312 168 0.1175 0.1244 REMARK 3 16 1.5600 - 1.5300 1.00 3385 138 0.1196 0.1330 REMARK 3 17 1.5300 - 1.5000 1.00 3330 165 0.1276 0.1383 REMARK 3 18 1.5000 - 1.4700 1.00 3335 155 0.1358 0.1415 REMARK 3 19 1.4700 - 1.4400 1.00 3320 182 0.1500 0.1734 REMARK 3 20 1.4400 - 1.4200 1.00 3325 151 0.1640 0.1809 REMARK 3 21 1.4200 - 1.4000 1.00 3362 156 0.1494 0.1674 REMARK 3 22 1.4000 - 1.3800 1.00 3332 169 0.1520 0.1852 REMARK 3 23 1.3800 - 1.3600 1.00 3357 161 0.1535 0.1556 REMARK 3 24 1.3600 - 1.3400 1.00 3310 166 0.1603 0.1681 REMARK 3 25 1.3400 - 1.3200 1.00 3335 176 0.1642 0.1675 REMARK 3 26 1.3200 - 1.3000 1.00 3323 166 0.1698 0.1854 REMARK 3 27 1.3000 - 1.2900 1.00 3301 160 0.1736 0.1720 REMARK 3 28 1.2900 - 1.2700 1.00 3318 197 0.1802 0.1962 REMARK 3 29 1.2700 - 1.2500 1.00 3290 188 0.1917 0.1930 REMARK 3 30 1.2500 - 1.2400 0.97 3229 153 0.2070 0.2040 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.084 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 3392 REMARK 3 ANGLE : 1.206 4640 REMARK 3 CHIRALITY : 0.092 506 REMARK 3 PLANARITY : 0.009 616 REMARK 3 DIHEDRAL : 19.992 1347 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5366 5.2350 -16.2325 REMARK 3 T TENSOR REMARK 3 T11: 0.0468 T22: 0.0533 REMARK 3 T33: 0.0522 T12: 0.0003 REMARK 3 T13: -0.0003 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.3448 L22: 0.3591 REMARK 3 L33: 0.2678 L12: -0.1160 REMARK 3 L13: 0.0977 L23: -0.0437 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.0176 S13: 0.0079 REMARK 3 S21: 0.0126 S22: 0.0168 S23: -0.0215 REMARK 3 S31: -0.0168 S32: 0.0337 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.3196 16.0667 -5.6100 REMARK 3 T TENSOR REMARK 3 T11: 0.0819 T22: 0.0900 REMARK 3 T33: 0.0687 T12: -0.0013 REMARK 3 T13: -0.0051 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.1150 L22: 0.1758 REMARK 3 L33: 0.2389 L12: 0.1219 REMARK 3 L13: -0.0019 L23: 0.0790 REMARK 3 S TENSOR REMARK 3 S11: -0.0279 S12: -0.0190 S13: 0.0734 REMARK 3 S21: 0.0356 S22: 0.0230 S23: -0.0429 REMARK 3 S31: -0.0505 S32: 0.1162 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9209 2.1197 -23.9383 REMARK 3 T TENSOR REMARK 3 T11: 0.0450 T22: 0.0610 REMARK 3 T33: 0.0655 T12: -0.0085 REMARK 3 T13: 0.0003 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.1347 L22: 0.4775 REMARK 3 L33: 0.2482 L12: -0.1746 REMARK 3 L13: 0.0255 L23: -0.0979 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: 0.0036 S13: 0.0129 REMARK 3 S21: -0.0152 S22: -0.0091 S23: -0.0484 REMARK 3 S31: 0.0094 S32: 0.0361 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9246 23.8948 -30.5809 REMARK 3 T TENSOR REMARK 3 T11: 0.0649 T22: 0.0547 REMARK 3 T33: 0.0733 T12: 0.0009 REMARK 3 T13: 0.0007 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.5173 L22: 0.7710 REMARK 3 L33: 0.3167 L12: -0.1207 REMARK 3 L13: 0.0892 L23: 0.0126 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: 0.0303 S13: 0.0857 REMARK 3 S21: -0.0707 S22: 0.0062 S23: 0.0150 REMARK 3 S31: -0.0819 S32: 0.0026 S33: -0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 245 THROUGH 341 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2783 1.9246 -31.7621 REMARK 3 T TENSOR REMARK 3 T11: 0.0584 T22: 0.0524 REMARK 3 T33: 0.0558 T12: -0.0064 REMARK 3 T13: 0.0040 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.3021 L22: 0.2725 REMARK 3 L33: 0.2126 L12: -0.1651 REMARK 3 L13: -0.0171 L23: 0.0493 REMARK 3 S TENSOR REMARK 3 S11: 0.0065 S12: 0.0264 S13: -0.0007 REMARK 3 S21: -0.0381 S22: -0.0062 S23: -0.0110 REMARK 3 S31: -0.0016 S32: 0.0237 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 342 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4052 -5.3422 -38.6367 REMARK 3 T TENSOR REMARK 3 T11: 0.1214 T22: 0.1103 REMARK 3 T33: 0.0961 T12: 0.0186 REMARK 3 T13: 0.0204 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.1663 L22: 0.1415 REMARK 3 L33: 0.1227 L12: -0.0619 REMARK 3 L13: -0.0290 L23: -0.1091 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: 0.1659 S13: -0.0104 REMARK 3 S21: -0.1302 S22: -0.0559 S23: -0.1122 REMARK 3 S31: 0.1218 S32: 0.1326 S33: -0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4461 7.3695 -30.3281 REMARK 3 T TENSOR REMARK 3 T11: 0.0795 T22: 0.0832 REMARK 3 T33: 0.0959 T12: -0.0156 REMARK 3 T13: 0.0102 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.3732 L22: 0.2955 REMARK 3 L33: 0.2435 L12: 0.0204 REMARK 3 L13: 0.1953 L23: -0.1805 REMARK 3 S TENSOR REMARK 3 S11: -0.0497 S12: 0.0587 S13: 0.0944 REMARK 3 S21: -0.0400 S22: 0.0200 S23: -0.1112 REMARK 3 S31: -0.0560 S32: 0.0782 S33: -0.0021 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7KDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97922 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 30.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2P02 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM CHLORIDE, 0.1 M TRIS PH REMARK 280 7.8, 24% PEG 6000, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.05500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.01350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.39750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.05500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.01350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.39750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.05500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.01350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.39750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.05500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.01350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.39750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 636 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 650 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 659 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 852 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 988 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 995 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1004 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 PHE A 8 REMARK 465 HIS A 9 REMARK 465 GLU A 10 REMARK 465 ALA A 11 REMARK 465 PHE A 12 REMARK 465 ILE A 13 REMARK 465 GLU A 14 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 373 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HE21 GLN A 190 H121 WBS A 401 1.28 REMARK 500 O HOH A 578 O HOH A 796 1.77 REMARK 500 O HOH A 615 O HOH A 681 1.87 REMARK 500 O HOH A 872 O HOH A 891 1.93 REMARK 500 O HOH A 783 O HOH A 877 1.93 REMARK 500 O HOH A 949 O HOH A 953 2.01 REMARK 500 O HOH A 531 O HOH A 824 2.03 REMARK 500 O HOH A 629 O HOH A 691 2.06 REMARK 500 O HOH A 985 O HOH A 990 2.08 REMARK 500 O HOH A 542 O HOH A 906 2.08 REMARK 500 O HOH A 847 O HOH A 874 2.10 REMARK 500 O HOH A 517 O HOH A 788 2.10 REMARK 500 NZ LYS A 391 O HOH A 501 2.11 REMARK 500 OE2 GLU A 147 O HOH A 502 2.16 REMARK 500 OE2 GLU A 85 O HOH A 503 2.16 REMARK 500 O HOH A 643 O HOH A 722 2.17 REMARK 500 O HOH A 606 O HOH A 684 2.17 REMARK 500 O HOH A 655 O HOH A 760 2.19 REMARK 500 O HOH A 834 O HOH A 847 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HD22 ASN A 105 HD22 ASN A 105 3555 1.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 134 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 PHE A 250 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 226 -67.60 -109.52 REMARK 500 THR A 270 -100.40 -116.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1009 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A1010 DISTANCE = 6.14 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue WBS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KCC RELATED DB: PDB REMARK 900 7KCC CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND AG-270 REMARK 900 RELATED ID: 7KCE RELATED DB: PDB REMARK 900 7KCE CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND 2 REMARK 900 RELATED ID: 7KCF RELATED DB: PDB REMARK 900 7KCF CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND 24512 REMARK 900 RELATED ID: 7KDA RELATED DB: PDB REMARK 900 7KDA CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND 34 DBREF 7KDB A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 7KDB SER A 0 UNP P31153 EXPRESSION TAG SEQRES 1 A 396 SER MET ASN GLY GLN LEU ASN GLY PHE HIS GLU ALA PHE SEQRES 2 A 396 ILE GLU GLU GLY THR PHE LEU PHE THR SER GLU SER VAL SEQRES 3 A 396 GLY GLU GLY HIS PRO ASP LYS ILE CYS ASP GLN ILE SER SEQRES 4 A 396 ASP ALA VAL LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP SEQRES 5 A 396 ALA LYS VAL ALA CYS GLU THR VAL ALA LYS THR GLY MET SEQRES 6 A 396 ILE LEU LEU ALA GLY GLU ILE THR SER ARG ALA ALA VAL SEQRES 7 A 396 ASP TYR GLN LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE SEQRES 8 A 396 GLY TYR ASP ASP SER SER LYS GLY PHE ASP TYR LYS THR SEQRES 9 A 396 CYS ASN VAL LEU VAL ALA LEU GLU GLN GLN SER PRO ASP SEQRES 10 A 396 ILE ALA GLN GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP SEQRES 11 A 396 ILE GLY ALA GLY ASP GLN GLY LEU MET PHE GLY TYR ALA SEQRES 12 A 396 THR ASP GLU THR GLU GLU CYS MET PRO LEU THR ILE VAL SEQRES 13 A 396 LEU ALA HIS LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG SEQRES 14 A 396 ARG ASN GLY THR LEU PRO TRP LEU ARG PRO ASP SER LYS SEQRES 15 A 396 THR GLN VAL THR VAL GLN TYR MET GLN ASP ARG GLY ALA SEQRES 16 A 396 VAL LEU PRO ILE ARG VAL HIS THR ILE VAL ILE SER VAL SEQRES 17 A 396 GLN HIS ASP GLU GLU VAL CYS LEU ASP GLU MET ARG ASP SEQRES 18 A 396 ALA LEU LYS GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA SEQRES 19 A 396 LYS TYR LEU ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SEQRES 20 A 396 SER GLY ARG PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA SEQRES 21 A 396 GLY LEU THR GLY ARG LYS ILE ILE VAL ASP THR TYR GLY SEQRES 22 A 396 GLY TRP GLY ALA HIS GLY GLY GLY ALA PHE SER GLY LYS SEQRES 23 A 396 ASP TYR THR LYS VAL ASP ARG SER ALA ALA TYR ALA ALA SEQRES 24 A 396 ARG TRP VAL ALA LYS SER LEU VAL LYS GLY GLY LEU CYS SEQRES 25 A 396 ARG ARG VAL LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SEQRES 26 A 396 SER HIS PRO LEU SER ILE SER ILE PHE HIS TYR GLY THR SEQRES 27 A 396 SER GLN LYS SER GLU ARG GLU LEU LEU GLU ILE VAL LYS SEQRES 28 A 396 LYS ASN PHE ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP SEQRES 29 A 396 LEU ASP LEU LYS LYS PRO ILE TYR GLN ARG THR ALA ALA SEQRES 30 A 396 TYR GLY HIS PHE GLY ARG ASP SER PHE PRO TRP GLU VAL SEQRES 31 A 396 PRO LYS LYS LEU LYS TYR HET WBS A 401 55 HET CL A 402 1 HET TRS A 403 14 HET EDO A 404 7 HET EDO A 405 7 HET GOL A 406 8 HET CL A 407 1 HET EDO A 408 10 HET SAM A 409 49 HETNAM WBS 6-(4-HYDROXYPHENYL)-2,3-DIPHENYL-5-[(1H-PYRAZOL-3-YL) HETNAM 2 WBS AMINO]PYRAZOLO[1,5-A]PYRIMIDIN-7(4H)-ONE HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM SAM S-ADENOSYLMETHIONINE HETSYN TRS TRIS BUFFER HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 WBS C27 H20 N6 O2 FORMUL 3 CL 2(CL 1-) FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 EDO 3(C2 H6 O2) FORMUL 7 GOL C3 H8 O3 FORMUL 10 SAM C15 H22 N6 O5 S FORMUL 11 HOH *510(H2 O) HELIX 1 AA1 HIS A 29 ASP A 49 1 21 HELIX 2 AA2 ASP A 78 GLY A 91 1 14 HELIX 3 AA3 SER A 95 GLY A 98 5 4 HELIX 4 AA4 SER A 114 HIS A 122 1 9 HELIX 5 AA5 ASN A 126 ILE A 130 5 5 HELIX 6 AA6 PRO A 151 ASN A 170 1 20 HELIX 7 AA7 CYS A 214 LYS A 225 1 12 HELIX 8 AA8 VAL A 226 VAL A 231 1 6 HELIX 9 AA9 PRO A 232 LEU A 236 5 5 HELIX 10 AB1 GLY A 253 GLY A 257 5 5 HELIX 11 AB2 LYS A 289 GLY A 308 1 20 HELIX 12 AB3 SER A 341 PHE A 353 1 13 HELIX 13 AB4 ARG A 356 ASP A 365 1 10 HELIX 14 AB5 ILE A 370 ALA A 375 5 6 HELIX 15 AB6 PHE A 385 VAL A 389 5 5 SHEET 1 AA1 4 THR A 17 VAL A 25 0 SHEET 2 AA1 4 LEU A 176 ASP A 191 -1 O TYR A 188 N PHE A 18 SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O ILE A 198 N GLN A 187 SHEET 4 AA1 4 ILE A 241 LEU A 244 1 O HIS A 243 N ILE A 203 SHEET 1 AA2 4 ASN A 105 GLU A 111 0 SHEET 2 AA2 4 MET A 64 THR A 72 1 N LEU A 67 O ALA A 109 SHEET 3 AA2 4 LYS A 53 LYS A 61 -1 N LYS A 53 O THR A 72 SHEET 4 AA2 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60 SHEET 1 AA3 2 ASP A 93 ASP A 94 0 SHEET 2 AA3 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94 SHEET 1 AA4 3 GLY A 136 THR A 143 0 SHEET 2 AA4 3 ARG A 313 TYR A 320 -1 O VAL A 316 N GLY A 140 SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O SER A 331 N GLN A 317 SITE 1 AC1 17 PHE A 18 PHE A 20 GLN A 190 ARG A 192 SITE 2 AC1 17 GLY A 193 ALA A 194 GLY A 273 TRP A 274 SITE 3 AC1 17 ARG A 313 LEU A 315 SER A 331 ILE A 332 SITE 4 AC1 17 PHE A 333 GLU A 342 EDO A 408 HOH A 560 SITE 5 AC1 17 HOH A 801 SITE 1 AC2 5 HIS A 29 ASP A 134 LYS A 181 LYS A 265 SITE 2 AC2 5 SAM A 409 SITE 1 AC3 5 ALA A 86 GLN A 372 HOH A 608 HOH A 640 SITE 2 AC3 5 HOH A 855 SITE 1 AC4 8 GLY A 91 LYS A 97 ARG A 168 LEU A 176 SITE 2 AC4 8 ARG A 177 PRO A 178 HOH A 521 HOH A 842 SITE 1 AC5 7 ARG A 219 HIS A 243 LEU A 244 PRO A 246 SITE 2 AC5 7 HOH A 513 HOH A 654 HOH A 848 SITE 1 AC6 11 ASP A 124 ARG A 125 ASN A 126 LYS A 228 SITE 2 AC6 11 ALA A 229 VAL A 230 VAL A 231 PRO A 232 SITE 3 AC6 11 HOH A 504 HOH A 566 HOH A 619 SITE 1 AC7 4 ARG A 177 GLU A 211 HOH A 507 HOH A 693 SITE 1 AC8 7 GLY A 193 PHE A 333 TYR A 335 WBS A 401 SITE 2 AC8 7 HOH A 524 HOH A 583 HOH A 636 SITE 1 AC9 22 HIS A 29 PRO A 30 ALA A 55 GLU A 70 SITE 2 AC9 22 GLN A 113 ASP A 116 ILE A 117 GLY A 133 SITE 3 AC9 22 ASP A 134 ASP A 179 LYS A 181 SER A 247 SITE 4 AC9 22 ARG A 249 PHE A 250 ASP A 258 LYS A 289 SITE 5 AC9 22 CL A 402 HOH A 609 HOH A 663 HOH A 667 SITE 6 AC9 22 HOH A 680 HOH A 736 CRYST1 68.110 94.027 116.795 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014682 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008562 0.00000